Figure 4.

The proposed slip-structure mechanism for allosteric regulation mediated by the class I induction element (A) and class II inhibition element (B) is illustrated. Shown are the proposed stem II secondary structures of the ligand-bound and unbound states of the FMN-modulated ribozymes. Not depicted are the left- and right-flanking sequences which comprise the aptamer and ribozyme domains, respectively. Asterisks denote the G and C residues of the hammerhead ribozyme that must pair to support catalysis, and the A and G residues of the FMN aptamer that become paired on ligand binding. Also shown are bimolecular ribozyme constructs containing stem II elements designed to simulate the active or inactive slip structures proposed for the class I induction module (C; I-1 through I-3) or the class II inhibition module (D; II-1 and II-2). Thick lines identify nucleotides that form the bridge elements. Mutations made within I-3 to reinforce the desired base pairing conformation are encircled.